PROJECT 3 This project's goal is to resolve the sequence structure of 20 complex genomic regions where common genome structural variation is associated with disease. In collaboration with Chris Amemiya, we propose to construct large-insert clone (BAC) libraries (10-fold coverage) from 18 reference genomes from the 1000 Genomes Project. We will target regions and individuals identified from Projects 1 and 2, retrieve and characterize BACs, and use next-generation sequencing (NGS) lllumina clone pooling strategy sequence to resolve haplotypes of these regions. As part of our collaboration with Washington University Genome Sequencing Center (WUGSC), we will select haplotype-resolved tiling paths for complete high-quality sequencing. The results of this work will provide common high-quality alternate haplotypes of biomedical relevance to be integrated into the human reference genome.